Matched Filter Stochastic Background Characterization for Hyperspectral Target Detection

Algorithms exploiting hyperspectral imagery for target detection have continually evolved to provide improved detection results. Adaptive matched filters can be used to locate spectral targets by modeling scene background as either structured (geometric) with a set of endmembers (basis vectors) or as unstructured (stochastic) with a covariance or correlation matrix. These matrices are often calculated using all available pixels in a data set. In unstructured background research, various techniques for improving upon scene-wide methods have been developed, each involving either the removal of target signatures from the background model or the segmentation of image data into spatial or spectral subsets. Each of these methods increase the detection signal-to-background ratio (SBR) and the multivariate normality (MVN) of the data from which background statistics are calculated, thus increasing separation between target and non-target species in the detection statistic and ultimately improving thresholded target detection results. Such techniques for improved background characterization are widely practiced but not well documented or compared. This paper provides a review and comparison of methods in target exclusion, spatial subsetting and spectral pre-clustering, and introduces a new technique which combines these methods. The analysis provides insight into the merit of employing unstructured background characterization techniques, as well as limitations for their practical application

Estimating Anthropometric Marker Locations from 3-D LADAR Point Clouds

An area of interest for improving the identification portion of the system is in extracting anthropometric markers from a Laser Detection and Ranging (LADAR) point cloud. Analyzing anthropometrics markers is a common means of studying how a human moves and has been shown to provide good results in determining certain demographic information about the subject. This research examines a marker extraction method utilizing principal component analysis (PCA), self-organizing maps (SOM), alpha hulls, and basic anthropometric knowledge. The performance of the extraction algorithm is tested by performing gender classification with the calculated markers

Matched filter stochastic background characterization for hyperspectral target detection

Algorithms exploiting hyperspectral imagery for target detection have continually evolved to provide improved detection results. Adaptive matched filters, which may be derived in many different scientific fields, can be used to locate spectral targets by modeling scene background as either structured geometric) with a set of endmembers (basis vectors) or as unstructured stochastic) with a covariance matrix. In unstructured background research, various methods of calculating the background covariance matrix have been developed, each involving either the removal of target signatures from the background model or the segmenting of image data into spatial or spectral subsets. The objective of these methods is to derive a background which matches the source of mixture interference for the detection of sub pixel targets, or matches the source of false alarms in the scene for the detection of fully resolved targets. In addition, these techniques increase the multivariate normality of the data from which the background is characterized, thus increasing adherence to the normality assumption inherent in the matched filter and ultimately improving target detection results. Such techniques for improved background characterization are widely practiced but not well documented or compared. This thesis will establish a strong theoretical foundation, describing the necessary preprocessing of hyperspectral imagery, deriving the spectral matched filter, and capturing current methods of unstructured background characterization. The extensive experimentation will allow for a comparative evaluation of several current unstructured background characterization methods as well as some new methods which improve stochastic modeling of the background. The results will show that consistent improvements over the scene-wide statistics can be achieved through spatial or spectral subsetting, and analysis of the results provides insight into the tradespaces of matching the interference, background multivariate normality and target exclusion for these techniques

Improving Hyperspectral Subpixel Target Detection Using Hybrid Detection Space

A Hyper-Spectral Image (HSI) has high spectral and low spatial resolution. As a result, most targets exist as subpixels, which pose challenges in target detection. Moreover, limitation of target and background samples always hinders the target detection performance. In this thesis, a hybrid method for subpixel target detection of an HSI using minimal prior knowledge is developed. The Matched Filter (MF) and Adaptive Cosine Estimator (ACE) are two popular algorithms in HSI target detection. They have different advantages in differentiating target from background. In the proposed method, the scores of MF and ACE algorithms are used to construct a hybrid detection space. First, some high abundance target spectra are randomly picked from the scene to perform initial detection to determine the target and background subsets. Then, the reference target spectrum and background covariance matrix are improved iteratively, using the hybrid detection space. As the iterations continue, the reference target spectrum gets closer and closer to the central line that connects the centers of target and background and resulting in noticeable improvement in target detection. Two synthetic datasets and two real datasets are used in the experiments. The results are evaluated based on the mean detection rate, Receiver Operating Characteristic (ROC) curve and observation of the detection results. Compared to traditional MF and ACE algorithms with Reed-Xiaoli Detector (RXD) background covariance matrix estimation, the new method shows much better performance on all four datasets. This method can be applied in environmental monitoring, mineral detection, as well as oceanography and forestry reconnaissance to search for extremely small target distribution in a large scene

On the Use of Imaging Spectroscopy from Unmanned Aerial Systems (UAS) to Model Yield and Assess Growth Stages of a Broadacre Crop

Snap bean production was valued at $363 million in 2018. Moreover, the increasing need in food production, caused by the exponential increase in population, makes this crop vitally important to study. Traditionally, harvest time determination and yield prediction are performed by collecting limited number of samples. While this approach could work, it is inaccurate, labor-intensive, and based on a small sample size. The ambiguous nature of this approach furthermore leaves the grower with under-ripe and over-mature plants, decreasing the final net profit and the overall quality of the product. A more cost-effective method would be a site-specific approach that would save time and labor for farmers and growers, while providing them with exact detail to when and where to harvest and how much is to be harvested (while forecasting yield). In this study we used hyperspectral (i.e., point-based and image-based), as well as biophysical data, to identify spectral signatures and biophysical attributes that could schedule harvest and forecast yield prior to harvest. Over the past two decades, there have been immense advances in the field of yield and harvest modeling using remote sensing data. Nevertheless, there still exists a wide gap in the literature covering yield and harvest assessment as a function of time using both ground-based and unmanned aerial systems. There is a need for a study focusing on crop-specific yield and harvest assessment using a rapid, affordable system. We hypothesize that a down-sampled multispectral system, tuned with spectral features identified from hyperspectral data, could address the mentioned gaps. Moreover, we hypothesize that the airborne data will contain noise that could negatively impact the performance and the reliability of the utilized models. Thus, We address these knowledge gaps with three objectives as below: 1. Assess yield prediction of snap bean crop using spectral and biophysical data and identify discriminating spectral features via statistical and machine learning approaches. 2. Evaluate snap bean harvest maturity at both the plant growth stage and pod maturity level, by means of spectral and biophysical indicators, and identify the corresponding discriminating spectral features. 3. Assess the feasibility of using a deep learning architecture for reducing noise in the hyperspectral data. In the light of the mentioned objectives, we carried out a greenhouse study in the winter and spring of 2019, where we studied temporal change in spectra and physical attributes of snap-bean crop, from Huntington cultivar, using a handheld spectrometer in the visible- to shortwave-infrared domain (400-2500 nm). Chapter 3 of this dissertation focuses on yield assessment of the greenhouse study. Findings from this best-case scenario yield study showed that the best time to study yield is approximately 20-25 days prior to harvest that would give out the most accurate yield predictions. The proposed approach was able to explain variability as high as R2 = 0.72, with spectral features residing in absorption regions for chlorophyll, protein, lignin, and nitrogen, among others. The captured data from this study contained minimal noise, even in the detector fall-off regions. Moving the focus to harvest maturity assessment, Chapter 4 presents findings from this objective in the greenhouse environment. Our findings showed that four stages of maturity, namely vegetative growth, budding, flowering, and pod formation, are distinguishable with 79% and 78% accuracy, respectively, via the two introduced vegetation indices, as snap-bean growth index (SGI) and normalized difference snap-bean growth index (NDSI), respectively. Moreover, pod-level maturity classification showed that ready-to-harvest and not-ready-to-harvest pods can be separated with 78% accuracy with identified wavelengths residing in green, red edge, and shortwave-infrared regions. Moreover, Chapters 5 and 6 focus on transitioning the learned concepts from the mentioned greenhouse scenario to UAS domain. We transitioned from a handheld spectrometer in the visible to short-wave infrared domain (400-2500 nm) to a UAS-mounted hyperspectral imager in the visible-to-near-infrared region (400-1000 nm). Two years worth of data, at two different geographical locations, were collected in upstate New York and examined for yield modeling and harvest scheduling objectives. For analysis of the collected data, we introduced a feature selection library in Python, named “Jostar”, to identify the most discriminating wavelengths. The findings from the yield modeling UAS study show that pod weight and seed length, as two different yield indicators, can be explained with R2 as high as 0.93 and 0.98, respectively. Identified wavelengths resided in blue, green, red, and red edge regions, and 44-55 days after planting (DAP) showed to be the optimal time for yield assessment. Chapter 6, on the other hand, evaluates maturity assessment, in terms of pod classification, from the UAS perspective. Results from this study showed that the identified features resided in blue, green, red, and red-edge regions, contributing to F1 score as high as 0.91 for differentiating between ready-to-harvest vs. not ready-to-harvest. The identified features from this study is in line with those detected from the UAS yield assessment study. In order to have a parallel comparison of the greenhouse study against the UAS study, we adopted the methodology employed for UAS studies and applied it to the greenhouse studies, in Chapter 7. Since the greenhouse data were captured in the visible-to-shortwave-infrared (400-2500 nm) domain, and the UAS study data were captured in the VNIR (400-1000 nm) domain, we truncated the spectral range of the collected data from the greenhouse study to the VNIR domain. The comparison experiment between the greenhouse study and the UAS studies for yield assessment, at two harvest stages early and late, showed that spectral features in 450-470, 500-520, 650, 700-730 nm regions were repeated on days with highest coefficient of determination. Moreover, 46-48 DAP with high coefficient of determination for yield prediction were repeated in five out of six data sets (two early stages, each three data sets). On the other hand, the harvest maturity comparison between the greenhouse study and the UAS data sets showed that similar identified wavelengths reside in ∼450, ∼530, ∼715, and ∼760 nm regions, with performance metric (F1 score) of 0.78, 0.84, and 0.9 for greenhouse, 2019 UAS, and 2020 UAS data, respectively. However, the incorporated noise in the captured data from the UAS study, along with the high computational cost of the classical mathematical approach employed for denoising hyperspectral data, have inspired us to leverage the computational performance of hyperspectral denoising by assessing the feasibility of transferring the learned concepts to deep learning models. In Chapter 8, we approached hyperspectral denoising in spectral domain (1D fashion) for two types of noise, integrated noise and non-independent and non-identically distributed (non-i.i.d.) noise. We utilized Memory Networks due to their power in image denoising for hyperspectral denoising, introduced a new loss and benchmarked it against several data sets and models. The proposed model, HypeMemNet, ranked first - up to 40% in terms of signal-to-noise ratio (SNR) for resolving integrated noise, and first or second, by a small margin for resolving non-i.i.d. noise. Our findings showed that a proper receptive field and a suitable number of filters are crucial for denoising integrated noise, while parameter size was shown to be of the highest importance for non-i.i.d. noise. Results from the conducted studies provide a comprehensive understanding encompassing yield modeling, harvest scheduling, and hyperspectral denoising. Our findings bode well for transitioning from an expensive hyperspectral imager to a multispectral imager, tuned with the identified bands, as well as employing a rapid deep learning model for hyperspectral denoising

Data-analysis strategies for image-based cell profiling

Image-based cell profiling is a high-throughput strategy for the quantification of phenotypic differences among a variety of cell populations. It paves the way to studying biological systems on a large scale by using chemical and genetic perturbations. The general workflow for this technology involves image acquisition with high-throughput microscopy systems and subsequent image processing and analysis. Here, we introduce the steps required to create high-quality image-based (i.e., morphological) profiles from a collection of microscopy images. We recommend techniques that have proven useful in each stage of the data analysis process, on the basis of the experience of 20 laboratories worldwide that are refining their image-based cell-profiling methodologies in pursuit of biological discovery. The recommended techniques cover alternatives that may suit various biological goals, experimental designs, and laboratories' preferences.Peer reviewe

A Novel Synergistic Model Fusing Electroencephalography and Functional Magnetic Resonance Imaging for Modeling Brain Activities

Study of the human brain is an important and very active area of research. Unraveling the way the human brain works would allow us to better understand, predict and prevent brain related diseases that affect a significant part of the population. Studying the brain response to certain input stimuli can help us determine the involved brain areas and understand the mechanisms that characterize behavioral and psychological traits. In this research work two methods used for the monitoring of brain activities, Electroencephalography (EEG) and functional Magnetic Resonance (fMRI) have been studied for their fusion, in an attempt to bridge together the advantages of each one. In particular, this work has focused in the analysis of a specific type of EEG and fMRI recordings that are related to certain events and capture the brain response under specific experimental conditions. Using spatial features of the EEG we can describe the temporal evolution of the electrical field recorded in the scalp of the head. This work introduces the use of Hidden Markov Models (HMM) for modeling the EEG dynamics. This novel approach is applied for the discrimination of normal and progressive Mild Cognitive Impairment patients with significant results. EEG alone is not able to provide the spatial localization needed to uncover and understand the neural mechanisms and processes of the human brain. Functional Magnetic Resonance imaging (fMRI) provides the means of localizing functional activity, without though, providing the timing details of these activations. Although, at first glance it is apparent that the strengths of these two modalities, EEG and fMRI, complement each other, the fusion of information provided from each one is a challenging task. A novel methodology for fusing EEG spatiotemporal features and fMRI features, based on Canonical Partial Least Squares (CPLS) is presented in this work. A HMM modeling approach is used in order to derive a novel feature-based representation of the EEG signal that characterizes the topographic information of the EEG. We use the HMM model in order to project the EEG data in the Fisher score space and use the Fisher score to describe the dynamics of the EEG topography sequence. The correspondence between this new feature and the fMRI is studied using CPLS. This methodology is applied for extracting features for the classification of a visual task. The results indicate that the proposed methodology is able to capture task related activations that can be used for the classification of mental tasks. Extensions on the proposed models are examined along with future research directions and applications